Hi Almudena, I think we would need to know what the model and map look like before refinement. I am guessing that perhaps the result from autosol was in itself not good, and then refinement could not do anything with it? If instead the autosol result was good (a clear map, a model that looks like you expect) then this is indeed very surprising and we'd be more than happy to try and figure out what is going on. All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Almudena Ponce Salvatierra [[email protected]] Sent: Saturday, January 24, 2015 1:08 AM To: [email protected] Subject: [phenixbb] Problem during refinement Dear all, I have partially rebuilt my model after autosol and now I would like to submit it for refinement to Phenix refine. However when I do so, even though the R factors go down when I have a look at the result, it just looks awful! All the model is placed out of the electron density map, plus the electron density map doesn't look anymore like a 3 A one, but just like sausages. Why is this happening? The truth is I have no idea... What I do is to provide Phenix refine with overall_best_refine_data.mtz (coming from autosol) as phases, x Ray data and x Ray r free data. Additionally, the starting model and the sequence. Any suggestions are more than welcome. Thanks a lot in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany